Objective To investigate the clinical effects of modified longitudinal section and and transverse suture and anal fissure resection on anal fissure. Methods A total of 98 patients with anal fissure from December 2015 to December 2020 were selected as study subjects and randomly divided into a control group （n=49） and an observation group （n=49）. The control group was treated with anal fissure resection, and the observation group was treated with modified longitudinal section and transverse suture. The clinical treatment effectiveness, complications after treatment, anal canal diameter changes, and incision healing time of the two groups were compared. Results The total effective rate of the observation group was 91.84%, higher than that of the control group （84.44%, P<0.05）. The observation group’s total incidence rate of edema, pain, infection, hematochezia, and constipation was 8.16%, lower than that of the control group （36.73%, P<0.05）. The diameter index of anal canal was increased in both groups, and the clinical treatment effect of the observation group was significantly higher than that of the control group （P<0.05）, while the wound healing time of observation group was shorter （P<0.05）. Conclusion Both the modified longitudinal section and transverse suture and the anal fissure resection can treat patients with anal fissure, but the former surgery can significantly improve clinical therapeutic effects, reduce the incidence of postoperative complications, and relieve pain, which is worthy of popularization and application.